To clarify the mechanisms underlying the differential response of cancer cells to photon and heavy ion irradiation, we performed RNA sequencing on NSCLC A549 cells exposed to X-rays and carbon ions and found that carbon ion irradiation induced a significant decrease in the expression of lncRNA EBLN3P (LNC EBLN3P) compared to X-rays in A549 cells. Here, EBLN3P is linked to cancer.